Firstly, I'm ashamed to say it has taken me since LXF 103 to pursue Mike Saunders's strong recommendation to try IceWM. But he's so right and it is a cracking little window manager (even doing tiling as well!).

What happens is that every so often the programs in the startup file get loaded, but their icons don't appear in the system tray. Instead a little indestructible black window appears. On restarting X, it always seems to correct itself. (For me it seems to happen after a power-on.)

The solution from the second Arch thread above is to put a "sleep 1" before every command in the startup file which puts an icon in the system tray. For example: